Mercurial > repos > elixir-it > covacs_apply_recalibrator
changeset 1:48dc4c9bc497 draft
Uploaded
| author | elixir-it |
|---|---|
| date | Thu, 15 Nov 2018 15:54:51 -0500 |
| parents | c785cec34cdc |
| children | f47e8d9b7f2e |
| files | mv_untar_gatk.sh tool-data/covacs_bed.loc.sample tool-data/covacs_gatk_indexes.loc.sample |
| diffstat | 3 files changed, 8 insertions(+), 7 deletions(-) [+] |
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--- a/mv_untar_gatk.sh Fri Nov 09 05:27:39 2018 -0500 +++ b/mv_untar_gatk.sh Thu Nov 15 15:54:51 2018 -0500 @@ -2,8 +2,9 @@ #if the .jar file is not present in the conda_prefix the script search the tar.gz in the conda_prefix of the vm #and untar the archive if [[ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ]] ; then - tar -zxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.gz -C $CONDA_PREFIX/../../ - + tar -jxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.bz2 --strip-components=1 -C $CONDA_PREFIX/../../ 2> log_tar + else - echo GATK is present + echo GATK is present fi +
--- a/tool-data/covacs_bed.loc.sample Fri Nov 09 05:27:39 2018 -0500 +++ b/tool-data/covacs_bed.loc.sample Thu Nov 15 15:54:51 2018 -0500 @@ -13,5 +13,5 @@ #is the value stored in the workflow for that parameter. That is why the #hg19 entry above looks odd. New genomes can be better-looking. # -hg19 hg19 hg19-padded /export/BED/S07084713_Padded.bed -hgbed hg19 hg19-bed-test /export/BED/chr22.bed +#hg19 hg19 hg19-padded /export/BED/S07084713_Padded.bed +#hgbed hg19 hg19-bed-test /export/BED/chr22.bed
--- a/tool-data/covacs_gatk_indexes.loc.sample Fri Nov 09 05:27:39 2018 -0500 +++ b/tool-data/covacs_gatk_indexes.loc.sample Thu Nov 15 15:54:51 2018 -0500 @@ -32,5 +32,5 @@ #is the value stored in the workflow for that parameter. That is why the #hg19 entry above looks odd. New genomes can be better-looking. # -hg38 hg38 hg38_GDC /export/gatkhg38pl/GRCh38.d1.vd1.fa -hg19 hg19 hg19 /export/gatk_hg19_index_bundle/ucsc.hg19.fasta +#hg38 hg38 hg38_GDC /export/gatkhg38pl/GRCh38.d1.vd1.fa +#hg19 hg19 hg19 /export/gatk_hg19_index_bundle/ucsc.hg19.fasta